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  • Jan 31 2019 22:37

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    Reports fix. Clear up issue in Galaxy docker… More reports fixes... and 1 more (compare)

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Martin Cech
@martenson
I knew Gitlab has it
Helena Rasche
@hexylena
GH does too, pretty nice.
Martin Cech
@martenson
I guess the higherlevel point was that there is no self-hosted github if they move towards monetization
Helena Rasche
@hexylena
bridge to cross later, if it happens :)
Marius van den Beek
@mvdbeek
They have been monetzing for a long time with github enterprise
Martin Cech
@martenson
@hexylena I am not ringing alarm bells :)
just getting my alarm bell hammer ready
Tomas
@TKlingstrom
The good thing with Github being owned by Microsoft is that Microsoft got so many other ways to monetize things that they probably use it as a free educational tool to capture all students who then move on to companies needing the Enterprise version :).
Saskia Hiltemann
@shiltemann

Hi GTN, @/all!

This February (15-19), we are organising a Global GTN training event! (Course Website)

All the training sessions will be pre-recorded, and participants from any time zone can join and work through these tutorials at their own pace, with support from instructors available on Slack.

The program includes an introduction to Galaxy, NGS Analyses (DNA-Seq and RNA-Seq) and Proteomics. The last day will be a "Choose Your Own Adventure" day, where participants can choose which GTN tutorials they would like to follow (including yours?).

Two things I would like to ask you all:

  1. Would you be willing to help answer participants questions during the workshop (via Slack) whenever you can during that week?
  2. Would you like to offer your tutorial as a training session on the "Choose your own adventure day"?

If you would like to be involved with this event in either of these ways, please see this document on how to proceed!

Thanks everybody! And please feel free to contact me with any questions you may have!

(If this workshop is successful, I am thinking we could make this an annual event, but maybe I am getting ahead of myself ;) This is just a really amazing community and I think we should show it off!)
Cristóbal Gallardo
@gallardoalba
Great, thanks!
Björn Grüning
@bgruening
@tnabtaf there is a new tutorial by @gallardoalba about metagenomics and Nanopore: https://github.com/galaxyproject/training-material/pull/2137/files
(unfortunately, we have Travis problems, I just contacted them, but it will not be online today)
Dave Clements
@tnabtaf
Thanks @bgruening (and thanks @gallardoalba !)
Cristóbal Gallardo
@gallardoalba
:)
Helena Rasche
@hexylena
per a top tip from @nsoranzo, the GTN isn't building due to being part of the galaxyproject travis account
image.png
We'll look into the options for deployment here
Esteban
@estebanpw

hello!
is there any way I can reference the slides corresponding to the hands on (i.e. in the same folder)? something like:

requirements:
  -
    type: "internal"
    topic_name: sequence_analysis
    slides:
      - <name_of_slides_in_current_tutorial_folder>

or is it only for other tutorials?

Helena Rasche
@hexylena
I don't think it's currently possible, most people just refer to the tutorial, and it's somewhat assumed you'll read the introductory slide deck for the tutorial you're doing?
Esteban
@estebanpw
I was thinking about people who might reach the hands on their own outside of a workshop. But I guess that if they manage to run the hands on they will also manage to read the slides :)
Saskia Hiltemann
@shiltemann
The slides will already be listed under "supporting material" in the box at the top too
Esteban
@estebanpw

The slides will already be listed under "supporting material" in the box at the top too

oops, didnt see that. Thats what I was looking for, thank you

Saskia Hiltemann
@shiltemann
:+1:
Dave Clements
@tnabtaf
@gallardoalba Tweet going out on your Monday morning.
2020-11-27_18-56-33-parque.png
Cristóbal Gallardo
@gallardoalba
Great, thanks @tnabtaf!
Saskia Hiltemann
@shiltemann

Hi @/all! As you may know, we are running a global online 5-day GTN training event in February (course webpage), featuring a "choose your own adventure" day.

Participants have (so far) indicated an interest in the following topics/tutorials for this CYOA day in the registration form:

  • Genome Annotation
  • Genome Assembly
  • Machine Learning
  • Chip-seq
  • RAD-seq
  • using workflow parameters
  • Epigenomics (ATAC seq analysis)
  • Imaging
  • GO-enrichment analysis
  • RNA-sequencing with alternative splicing
  • Variant Analysis
  • RNA-seq genes to pathways.

So if anybody is interested in teaching one of these topics (or any other), please let us know and we will add it to the program! This would involve being available to help with support on Slack on the day of workshop (Feb 19), and recording a video of the tutorial (video is optional, but we expect more people will follow your tutorial if there is a recording).

We expect a lot of participants, and all videos will stay up after the event as a self-study course, so this is a great way to show off our tutorials to a global audience!

We are also looking for any instructors willing to help out just by keeping an eye on Slack that week and help answer questions when they can.

If you are interested in being involved, please let us know here, or join our Slack channel and say hi the #instructors channel

Cristóbal Gallardo
@gallardoalba
Hi @shiltemann, I'm interested in teaching genome assembly.
Saskia Hiltemann
@shiltemann
@gallardoalba awesome! Did you already have a GTN tutorial in mind for this?
Cristóbal Gallardo
@gallardoalba
Should I record just one video or could I choose a couple of trainings in order to work with different tools?
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads would be my first option
Saskia Hiltemann
@shiltemann
That is a cool tutorial! I think that would be really great, perhaps we can do a video of the intro to assembly slides as an introduction. My plan was to perhaps also do some basic assembly on the first day too, with @Slugger70 (it all depends a bit on how long all the sessions are, don't want to make the days too long), but then this would be a perfect "advanced assembly" tutorial for the last day
(I have some meetings now, but let's discuss this further soon! thanks!)
Pavankumar Videm
@pavanvidem
is there a training material available about workflow reports?
Björn Grüning
@bgruening
Not yet. @wm75 has some expertise.
Wolfgang Maier
@wm75
I could try putting a tutorial together, yes. Will probably need frequent updates. I'll give it a try next week.
Saskia Hiltemann
@shiltemann
@wm75 that would be great!
Pavankumar Videm
@pavanvidem
Thanks @wm75
Do we have an example or instructions somewhere?
Wolfgang Maier
@wm75
@pavanvidem Not really yet beyond what's discussed in PRs I think.
Torfinn Nome
@torfinnnome
So, uhm, hi. I hear a tutorial configuring Galaxy with Singularity would be useful (I totally agree). I might be able to contribute. But if this is to be used in a training session, it would be useful to know which OS to base this on, etc, so I can test it properly. I assume this should be based on the "Galaxy Installation with Ansible", and be a "Further Learning" tutorial?
Nicola Soranzo
@nsoranzo
Hi @torfinnnome , @hexylena is in charge but AFAIK your assumptions are correct. UseGalaxy.* normally provide VMs with Ubuntu, but we try to mention what's different when doing a tutorial step on a different OS, if needed and we are aware.
And thanks so much, I look forward to this tutorial myself!
Torfinn Nome
@torfinnnome
Right, ok, thanks, I'll give it a go. :)
Helena Rasche
@hexylena
@torfinnnome we'll be using the machines https://gxy.io/gatmachines, feel free to claim one to do your development on
that's super awesome :)
ping me if you have any questions!
Torfinn Nome
@torfinnnome
Ah, nice, that will be useful.